A revised dated phylogeny of the arachnid order Opiliones

Dating the Opiliones tree of life has become an important enterprise for this group of arthropods, due to their ancient origins and important biogeographic implications. To incorporate both methodological innovations in molecular dating as well as new systematic discoveries of harvestman diversity, we conducted total evidence dating on a data set uniting morphological and/or molecular sequence data for 47 Opiliones species, including all four well-known Palaeozoic fossils, to test the placement of both fossils and newly discovered lineages in a single analysis. Furthermore, we investigated node dating with a phylogenomic data set of 24,202 amino acid sites for 14 species of Opiliones, sampling all extant suborders. In this way, we approached molecular dating of basal harvestman phylogeny using different data sets and approaches to assess congruence of divergence time estimates. In spite of the markedly different composition of data sets, our results show congruence across all analyses for age estimates of basal nodes that are well constrained with respect to fossil calibrations (e.g., Opiliones, Palpatores). By contrast, derived nodes that lack fossil calibrations (e.g., the suborders Cyphophthalmi, and Laniatores) have large uncertainty intervals in diversification times, particularly in the total evidence dating analysis, reflecting the dearth of calibration points and undersampling of derived lineages. Total evidence dating consistently produced older median ages than node dating for ingroup nodes, due to the nested placement of multiple Palaeozoic fossils. Our analyses support basal diversification of Opiliones in the Ordovician-Devonian period, corroborating the inferred ancient origins of this arthropod order, and underscore the importance of diversity discovery—both paleontological and neontological—in evolutionary inference

Efficient tree searches with available algorithms

Phylogenetic methods based on optimality criteria are highly desirable for their logic properties, but time-consuming when compared to other methods of tree construction. Traditionally, researchers have been limited to exploring tree space by using multiple replicates of Wagner addition followed by typical hill climbing algorithms such as SPR or/and TBR branch swapping but these methods have been shown to be insuficient for “large” data sets (or even for small data sets with a complex tree space). Here, I review different algorithms and search strategies used for phylogenetic analysis with the aim of clarifying certain aspects of this important part of the phylogenetic inference exercise. The techniques discussed here apply to both major families of methods based on optimality criteria—parsimony and maximum likelihood—and allow the thorough analysis of complex data sets with hundreds to thousands of terminal taxa. A new technique, called pre-processed searches is proposed for reusing phylogenetic results obtained in previous analyses, to increase the applicability of the previously proposed jumpstarting phylogenetics method. This article is aimed to serve as an educational and algorithmic reference to biologists interested in phylogenetic analysis.Organismic and Evolutionary Biolog

Shearogovea, a New Genus of Cyphophthalmi (Arachnida, Opiliones) of Uncertain Position from Oaxacan Caves, Mexico

Shearogovea gen. nov. is erected for Neogovea mexasca Shear, 1977, a troglobitic cyphophthalmid species from a cave system in Oaxaca, Mexico. The new genus does not show affinity to Neogovea Hinton, 1938, as it lacks the characteristic toothed claw of leg II or the fusion of the coxae of legs II to those of legs III (which are in turn fused to coxae of legs IV). Shearogovea gen. nov. is probably not related to other Neotropical neogoveid genera, but its exact phylogenetic position remains unresolved.Organismic and Evolutionary Biolog

Current views on chelicerate phylogeny—A tribute to Peter Weygoldt

Peter Weygoldt pioneered studies of arachnid phylogeny by providing the first synapomorphy scheme to underpin inter-ordinal relationships. Since this seminal work, arachnid relationships have been evaluated using morphological characters of extant and fossil taxa as well as multiple generations of molecular sequence data. While nearly all datasets agree on the monophyly of Tetrapulmonata, and modern analyses of molecules and novel morphological and genomic data support Arachnopulmonata (a sister group relationship of Scorpiones to Tetrapulmonata), the relationships of the apulmonate arachnid orders remain largely unresolved. Three threads may allow us to resolve the recalcitrant phylogeny of arachnids: the careful evaluation of large amounts of molecular data; novel techniques grounded in comparative morphology and evolutionary developmental biology, which add improved homology statements and explain the transition between character states; and new fossil discoveries, which continue to incorporate relevant novel data to the discussion of the relationships among the arachnid orders.Organismic and Evolutionary Biolog

A dataset comprising four micro-computed tomography scans of freshly fixed and museum earthworm specimens

Background: Although molecular tools are increasingly employed to decipher invertebrate systematics, earthworm (Annelida: Clitellata: ‘Oligochaeta’) taxonomy is still largely based on conventional dissection, resulting in data that are mostly unsuitable for dissemination through online databases. In order to evaluate if micro-computed tomography (μCT) in combination with soft tissue staining techniques could be used to expand the existing set of tools available for studying internal and external structures of earthworms, μCT scans of freshly fixed and museum specimens were gathered. Findings: Scout images revealed full penetration of tissues by the staining agent. The attained isotropic voxel resolutions permit identification of internal and external structures conventionally used in earthworm taxonomy. The μCT projection and reconstruction images have been deposited in the online data repository GigaDB and are publicly available for download. Conclusions: The dataset presented here shows that earthworms constitute suitable candidates for μCT scanning in combination with soft tissue staining. Not only are the data comparable to results derived from traditional dissection techniques, but due to their digital nature the data also permit computer-based interactive exploration of earthworm morphology and anatomy. The approach pursued here can be applied to freshly fixed as well as museum specimens, which is of particular importance when considering the use of rare or valuable material. Finally, a number of aspects related to the deposition of digital morphological data are briefly discussed

On Speleosiro argasiformis—a troglobitic Cyphophthalmi (Arachnida: Opiliones: Pettalidae) from Table Mountain, South Africa

We report the recent collection and observation of large numbers of specimens of the troglobitic harvestman Speleosiro argasiformis Lawrence 1931 in the Wynberg Cave system, Table Mountain, South Africa. Specimens were collected and/or photographed in different caves of the system. Live observation showed specimens fleeing bat carcasses when disturbed.Organismic and Evolutionary Biolog

Monophyly, Taxon Sampling, and the Nature of Ranks in the Classification of Orb-Weaving Spiders (Araneae: Araneoidea)

Under embargo until: 2020-07-11We address some of the taxonomic and classification changes proposed by Kuntner et al. (2019) in a comparative study on the evolution of sexual size dimorphism in nephiline spiders. Their proposal to recircumscribe araneids and to rank the subfamily Nephilinae as a family is fundamentally flawed as it renders the family Araneidae paraphyletic. We discuss the importance of monophyly, outgroup selection, and taxon sampling, the subjectivity of ranks, and the implications of the age of origin criterion to assign categorical ranks in biological classifications. We explore the outcome of applying the approach of Kuntner et al. (2019) to the classification of spiders with emphasis on the ecribellate orb-weavers (Araneoidea) using a recently published dated phylogeny. We discuss the implications of including the putative sister group of Nephilinae (the sexually dimorphic genus Paraplectanoides) and the putative sister group of Araneidae (the miniature, monomorphic family Theridiosomatidae). We propose continuation of the phylogenetic classification put forth by Dimitrov et al. (2017), and we formally rank Nephilinae and Phonognathinae as subfamilies of Araneidae. Our classification better reflects the understanding of the phylogenetic placement and evolutionary history of nephilines and phonognathines while maintaining the diagnosability of Nephilinae. It also fulfills the fundamental requirement that taxa must be monophyletic, and thus avoids the paraphyly of Araneidae implied by Kuntner et al. (2019).acceptedVersio

An Anatomical Description of a Miniaturized Acorn Worm (Hemichordata, Enteropneusta) with Asexual Reproduction by Paratomy

The interstitial environment of marine sandy bottoms is a nutrient-rich, sheltered habitat whilst at the same time also often a turbulent, space-limited, and ecologically challenging environment dominated by meiofauna. The interstitial fauna is one of the most diverse on earth and accommodates miniaturized representatives from many macrofaunal groups as well as several exclusively meiofaunal phyla. The colonization process of this environment, with the restrictions imposed by limited space and low Reynolds numbers, has selected for great morphological and behavioral changes as well as new life history strategies. Here we describe a new enteropneust species inhabiting the interstices among sand grains in shallow tropical waters of the West Atlantic. With a maximum body length of 0.6 mm, it is the first microscopic adult enteropneust known, a group otherwise ranging from 2 cm to 250 cm in adult size. Asexual reproduction by paratomy has been observed in this new species, a reproductive mode not previously reported among enteropneusts. Morphologically, Meioglossus psammophilus gen. et sp. nov. shows closest resemblance to an early juvenile stage of the acorn worm family Harrimaniidae, a result congruent with its phylogenetic placement based on molecular data. Its position, clearly nested within the larger macrofaunal hemichordates, suggests that this represents an extreme case of miniaturization. The evolutionary pathway to this simple or juvenile appearance, as chiefly demonstrated by its small size, dense ciliation, and single pair of gill pores, may be explained by progenesis. The finding of M. psammophilus gen. et sp. nov. underscores the notion that meiofauna may constitute a rich source of undiscovered metazoan diversity, possibly disguised as juveniles of other species.Organismic and Evolutionary Biolog